Ch 2 Text 3

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  1. o   There are __, __, __, and __were identified. The turns and loops contribute with __ and __ to form the final protein structure
    §  They are formed by a regular pattern of hydrogen bonds between the peptide N—H and the C=O groups of amino acids that are __
    • alpha helices, Beta pleated sheet, beta turns, and omega loops 
    • alpha helices and Beta sheets 
    • near one another in the linear sequence
  2. Explain the alpha helix
    o   rodlike structure; a tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array

    •  It is stabilized by hydrogen bonds between the NH and CO groups of the main chain
  3. Alpha Helix:

    In particular, the __ group of each amino acid forms a hydrogen bond with the __group of the amino acid that is situated __ ahead in the sequence

    §  Thus, except for __, all the __ are __. Each residue is related to the next one by a rise, also called __, of 1.5 angstroms along the helix axis and a rotation of __, which gives __ per turn of helix
    • CO 
    • NH 
    • four residues
    • amino acids near the ends of an alpha helix
    • main-chain CO and NH groups are hydrogen bonded
    • translation
    • 100o
    • 3.6 amino acids residues
  4. §  Amino acids spaced __ in the sequence are spatially quite close to one another in an __
    · In contrast, amino acids spaced _ in the sequence are situated on __ of the helix and are unlikely to make contact
    o   What is the pitch of the alpha helix and what is it equal to?
    • three and four apart
    • alpha helix
    • two apart
    • opposite sides

    the length of one complete turn along the helix axis; it is equal to the product of the rise and the number of residues per turn
  5. §  The screw sense (describes the __) of a helix can be clockwise or counterclockwise, which are both allowed conformations
    ·         __ are energetically more favorable because of __
    · All alpha helices found in proteins are __
    direction in which a helical structure rotates with respect to its axis

    Right handed

    less steric collision

  6. §  Not all amino acids can be accommodated in an __. Branching at the __ atom does what (as in valine, threonine, and isoleucine)
    §  Serine, aspartate, and asparagine also tend to disrupt __ because their __ contain __, where they __
    • alpha helix
    • Beta-carbon
    • destabilizes alpha helices due to steric clashes
    • alpha helices
    • side chains
    • hydrogen-bond donors or acceptors in close proximity to the main chain
    • compete for main-chain NH and CO groups
  7. §  Proline also is a __ because it lacks an __ and because its __
    §  The alpha helical content of proteins ranges from none to almost 100%
    • helix breaker
    • NH group and because its ring structure prevents it from assuming the phi value to fit into an alpha helix
  8. Explain beta pleated sheets.
    o   differs from rodlike alpha helix and composed of two or more polypeptide chains called beta strands, which is almost fully extended (sterically allowed) rather than being tightly coiled as in the alpha helix 
  9. §  The distance between adjacent amino acids along the beta strand is __ angstroms; side chains are arranged how?
    §  Formed how?
    • 3.5
    • they point in opposite directions
    • by linking two or more beta strands lying next to one another through hydrogen bonds
  10. · Adjacent chains in a beta sheet can run in __ or __
    opposite directions (antiparallel B sheet) or in the same direction (parallel)
  11. Explain the antiparallel arrangement of beta sheets.
    o   the NH group and the CO group of each amino acid are respectively hydrogen bonded to the CO group and the NH group of a partner on the adjacent chain
  12. Explain the parallel arrangement of beta sheets.
    §  For each amino acid, the NH group is hydrogen bonded to the CO group of one amino acid on the adjacent strand, whereas the CO group is hydrogen bonded to the NH group on the amino acid two residues farther along the chain
  13. · Many strands can come together in beta sheets and they can be __ or __ or __
    §  In schematic representations, Beta strands are usually depicted how to indicate what?
    · They can be almost __ or __
    • purely anti or parallel or mixed
    • by broad arrows pointing in the direction of the carboxyl terminal end
    • the type of Beta sheet formed—parallel or antiparallel
    • flat or twisted
  14. o   Most proteins have compact, globular shapes owing to the __
    §  Many of these reversals are accomplished by a common structural element called the __
    reversals in the direction of their polypeptide chains

    reverse turn (Beta turn or hairpin turn)
  15. · In many reverse turns, the CO group of residue I of a polypeptide is hydrogen bonded to the NH group of residue __
    o   This interaction  does what?
    §  In other cases, more elaborate structures are responsible for chain reversals; these structures are called __
    · Unlike alpha helices and beta strands, __do not have __
    • i+ 3
    • stabilizes abrupt changes in direction of the polypeptide chain
    • loops or sometimes omega loops to suggest their overall shape
    • loops 
    • regular, periodic structures
  16. §  Nonetheless, loop structures are often __ and __

    · Turns and loops invariably lie where and thus often participate in what
    • rigid and well defined
    • on the surfaces of proteins
    • interactions between proteins and other molecules
  17. o   Fibrous proteins provide __ for cells and tissues
    §  Special types of helices are present in __ and __that form long fibers for structure
    · Alpha-keratin has __ intertwined to form a type of __ called an __
    • structural support
    • alpha-keratin
    • collagen 
    • two right-handed alpha helices
    • left-handed superhelix called an alpha-helical coiled coil
  18. o   It is a member of a superfamily of proteins called __ (about 60), where two __; __, _, and __ are included in this
    o   Characteristic of this family: what
    • coiled-coil proteins
    • + alpha helices can entwine to form a very stable structure
    • intermediate filaments, mysosin and tropomyosin
    • a central region of 300 amino acids with imperfect repeats of a sequence of seven amino acids called a heptad repeat
  19. o   The two helices in alpha keratin are cross-linked by __ (like vdW and ionic), which are facilitated by the fact that the __ alters the two __ such that there are 3.5 residues per turn instead of 3.6
    §  The pattern of side chain interactions can be repeated every __residues, forming the __
    • weak interactions
    • left-handed supercoil
    • right-handed alpha helices
    • seven 
    • heptad repeats
  20. ·         Two helices with such repeats are able to interact with one another if the repeats are __
    o   The repeating residues may be __, allowing for __, or have __, allowing __
    o   In addition, the two helices may be linked by __ formed by __
    • complementary
    • hydrophobic
    • vdW interactions
    • opposite charge
    • ionic interactions
    • disulfide bonds
    • neighboring cysteine residue
  21. o   The bonding of the helices accounts for the physical properties of wool, an example of an alpha-keratin; the __ stretch, breaking the weak interactions between neighboring helices. But, the __ resist breakage and return the fiber to its original state once stretching is released
    • alpha helices
    • covalent disulfide bonds
  22. · __is the main fibrous component of skin, bone, tendon, cartilage, and teeth; and, it is __, containing __, each __
    o   __is at every third residue; and the sequence __ (a derivative of proline with a –OH group in place of a hydrogen atom) recurs frequently
    • Collagen 
    • rod shaped, containing three helical polypeptide chains, each nearly 1000 residues long
    • Glycine 
    • glycine-proline-hydroxyproline
  23. o   The collagen helix has properties different from those of the alpha helix in that hydrogen bonds within the strand are absent. Instead, the helix is stabilized by __

    §  The __ keep out of each other’s way when the polypeptide chain assumes its __ form, which has about three residues per turn
    steric repulsion of the pyrrolidine rings of the proline and hydroxyproline residues

    pyrrolidine rings

  24. ·         Three strands wind around one another to form a __ that is stabilized by __ between strands
    o   The H bonds form between the __ and __
    • superhelical cable
    • hydrogen bonds
    • peptide NH groups of glycine residues and the CO groups of residues on the other chains
  25. o   The __ residues also participate in __, and the absence of the __ results in the disease __
    o   The inside of the triple-stranded helical cable is __ and accounts for the requirement that __. The only residue that can fit in an interior position is __
    • hydroxyl groups of hydroxyproline
    • hydrogen bonding
    • hydroxyl groups
    • scurvy
    • very crowded
    • glycine be present at every third position on each strand
    • glycine
  26. §  The amino acid residue on either side of it is __of the cable
    o   This lack of positioning results in diseases, such as __
    • outside 
    • osteogenesis imperfect
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Ch 2 Text 3
Test One
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